Abstract 404: Identification of combination partners to combat acquired resistance to ulixertinib (ERK1/2 inhibitor) using transcriptomics
Authors: Anupama Reddy, David Sorrell, Deborah Knoerzer, Caroline M. Emery
Journal: Cancer Research (2022)

Abstract Drug resistance is arguably the rate-limiting step in the successful clinical utility of MAPK inhibitors. Several mechanisms of resistance to BRAF and MEK inhibitors have been proposed, including feedback mechanisms and activation of complementary signaling pathways, which have led to the development of combination therapies. Ulixertinib (BVD-523), a first-in-class and ERK1/2 inhibitor, is clinically effective in patients with tumors harboring alterations in the MAPK pathway. In this project, we have developed resistance clones to ulixertinib and have identified mechanisms of acquired resistance using RNA-seq analysis, thus enabling us to identify potential combination partners to combat resistance. In vitro experiments were deployed to develop resistance models to ulixertinib. Resistance clones were developed by culturing A375 cell line (melanoma; BRAF V600E) in escalating concentrations of ulixertinib. RNA-sequencing was performed on the parental model and the resistance clones following varying treatment conditions with ulixertinib. RNAseq and principal component analysis revealed strong differences between parental and resistance clones, with further differentiation between acute high concentration and chronic treatment models compared to models treated with acute, lower concentrations of ulixertinib. These results highlight the presence of a dose-dependent resistance phenotype. Differential gene expression analysis revealed enrichment of several pathways, including MAPK, autophagy, focal adhesion, JAK/STAT, and VEGF. Interestingly, we observed rewiring of PI3K/AKT by shifting the signaling from EGFR to ERBB2 in the resistance models. The magnitude of changes in these genes and pathways also exhibited a dose-dependent effect, with higher concentration models showing a higher fold-change compared to the lower concentration models. We explored these hypotheses by performing combination experiments with ulixertinib in the generated resistance clones. Synergistic combination targets in the ulixertinib resistance clones included ERBB2, and FAK. We also validated combinations with autophagy inhibitors, one of which is now being tested in a Phase I clinical trial (NCT04145297). In summary, we have identified some potential resistance mechanisms to ulixertinib and have validated key genes/pathways which may act as synergistic combination targets. This work not only informs future clinical development for ulixertinib but also improves our understanding of the complex interplay between the MAPK and other signaling pathways. Citation Format: Anupama Reddy, David Sorrell, Deborah Knoerzer, Caroline M. Emery. Identification of combination partners to combat acquired resistance to ulixertinib (ERK1/2 inhibitor) using transcriptomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 404.